/*.................................................................................................................*/ void getArguments( MultipartEntityBuilder builder, StringBuffer sb, String fileName, String LOCproteinModel, String LOCdnaModel, String LOCotherOptions, int LOCbootstrapreps, int LOCbootstrapSeed, int LOCnumRuns, String LOCoutgroupTaxSetString, String LOCMultipleModelFile, boolean preflight) { if (builder == null) return; /* if (preflight) arguments += " -n preflight.out "; else arguments += " -s " + fileName + " -n file.out "; */ if (isProtein) { if (StringUtil.blank(LOCproteinModel)) addArgument(builder, sb, "vparam.protein_opts_", "PROTGAMMAJTT"); else addArgument(builder, sb, "vparam.protein_opts_", LOCproteinModel); } else if (StringUtil.blank(LOCdnaModel)) addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA"); else addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA"); // builder.addTextBody("vparam.dna_gtrcat_",LOCdnaModel); /* if (StringUtil.notEmpty(LOCMultipleModelFile)) arguments += " -q " + ShellScriptUtil.protectForShellScript(LOCMultipleModelFile); if (!StringUtil.blank(LOCotherOptions)) arguments += " " + LOCotherOptions; */ addArgument(builder, sb, "vparam.provide_parsimony_seed_", "1"); addArgument(builder, sb, "vparam.parsimony_seed_val_", "" + randomIntSeed); if (bootstrapOrJackknife()) { if (LOCbootstrapreps > 0) { addArgument(builder, sb, "vparam.choose_bootstrap_", "b"); addArgument(builder, sb, "vparam.bootstrap_value_", "" + LOCbootstrapreps); addArgument(builder, sb, "vparam.seed_value_", "" + LOCbootstrapSeed); // addArgument(builder, sb, "vparam.bootstrap_",""+LOCbootstrapreps); // addArgument(builder, sb, "vparam.mulparambootstrap_seed_",""+LOCbootstrapSeed); } else Debugg.println("TOO FEW BOOTSTRAP REPS"); } else { addArgument(builder, sb, "vparam.specify_runs_", "1"); addArgument(builder, sb, "vparam.altrun_number_", "" + LOCnumRuns); // if (RAxML814orLater) // addArgument(builder, sb, "vparam.mesquite_output_","1"); } TaxaSelectionSet outgroupSet = null; if (!StringUtil.blank(LOCoutgroupTaxSetString)) { outgroupSet = (TaxaSelectionSet) taxa.getSpecsSet(LOCoutgroupTaxSetString, TaxaSelectionSet.class); if (outgroupSet != null) addArgument(builder, sb, "vparam.outgroup_", outgroupSet.getStringList(",", true)); arguments += " -o " + outgroupSet.getStringList(",", true); } }